X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FHiddenColumnsTest.java;h=e6c9b32a51f125cdde5f8b158aa9599f47e9ffca;hb=b95ecdde59db976d721fe9aec626105947825b9e;hp=edd68b23c3dcf53df54568d5b4542f803175b934;hpb=af4abf989c69bbfaa30a25eff93133867bbce6c8;p=jalview.git diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java index edd68b2..e6c9b32 100644 --- a/test/jalview/datamodel/HiddenColumnsTest.java +++ b/test/jalview/datamodel/HiddenColumnsTest.java @@ -68,22 +68,22 @@ public class HiddenColumnsTest public void testFindColumnPosition() { HiddenColumns cs = new HiddenColumns(); - assertEquals(5, cs.findColumnPosition(5)); + assertEquals(5, cs.absoluteToVisibleColumn(5)); // hiding column 6 makes no difference cs.hideColumns(6, 6); - assertEquals(5, cs.findColumnPosition(5)); + assertEquals(5, cs.absoluteToVisibleColumn(5)); // hiding column 4 moves column 5 to column 4 cs.hideColumns(4, 4); - assertEquals(4, cs.findColumnPosition(5)); + assertEquals(4, cs.absoluteToVisibleColumn(5)); // hiding column 4 moves column 4 to position 3 - assertEquals(3, cs.findColumnPosition(4)); + assertEquals(3, cs.absoluteToVisibleColumn(4)); // hiding columns 1 and 2 moves column 5 to column 2 cs.hideColumns(1, 2); - assertEquals(2, cs.findColumnPosition(5)); + assertEquals(2, cs.absoluteToVisibleColumn(5)); // check with > 1 hidden column regions // where some columns are in the hidden regions @@ -93,25 +93,25 @@ public class HiddenColumnsTest cs2.hideColumns(40, 44); // hiding columns 5-10 and 20-27 moves column 8 to column 4 - assertEquals(4, cs2.findColumnPosition(8)); + assertEquals(4, cs2.absoluteToVisibleColumn(8)); // and moves column 24 to 13 - assertEquals(13, cs2.findColumnPosition(24)); + assertEquals(13, cs2.absoluteToVisibleColumn(24)); // and moves column 28 to 14 - assertEquals(14, cs2.findColumnPosition(28)); + assertEquals(14, cs2.absoluteToVisibleColumn(28)); // and moves column 40 to 25 - assertEquals(25, cs2.findColumnPosition(40)); + assertEquals(25, cs2.absoluteToVisibleColumn(40)); // check when hidden columns start at 0 that the visible column // is returned as 0 HiddenColumns cs3 = new HiddenColumns(); cs3.hideColumns(0, 4); - assertEquals(0, cs3.findColumnPosition(2)); + assertEquals(0, cs3.absoluteToVisibleColumn(2)); // check that column after the last hidden region doesn't crash - assertEquals(46, cs2.findColumnPosition(65)); + assertEquals(46, cs2.absoluteToVisibleColumn(65)); } @Test(groups = { "Functional" }) @@ -420,9 +420,9 @@ public class HiddenColumnsTest new SequenceI[] { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") }); HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(al.getSequenceAt(0)); + cs.hideList(al.getSequenceAt(0).getInsertions()); assertEquals("G", "" - + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9))); + + al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9))); // KM: no idea what this is meant to be testing... seems to be an unfinished // test @@ -689,40 +689,40 @@ public class HiddenColumnsTest // one hidden range one.set(1); cs = new HiddenColumns(); - cs.hideMarkedBits(one); + cs.hideColumns(one); assertEquals(1, cs.getNumberOfRegions()); one.set(2); cs = new HiddenColumns(); - cs.hideMarkedBits(one); + cs.hideColumns(one); assertEquals(1, cs.getNumberOfRegions()); one.set(3); cs = new HiddenColumns(); - cs.hideMarkedBits(one); + cs.hideColumns(one); assertEquals(1, cs.getNumberOfRegions()); // split one.clear(2); cs = new HiddenColumns(); - cs.hideMarkedBits(one); + cs.hideColumns(one); assertEquals(2, cs.getNumberOfRegions()); - assertEquals(0, cs.adjustForHiddenColumns(0)); - assertEquals(2, cs.adjustForHiddenColumns(1)); - assertEquals(4, cs.adjustForHiddenColumns(2)); + assertEquals(0, cs.visibleToAbsoluteColumn(0)); + assertEquals(2, cs.visibleToAbsoluteColumn(1)); + assertEquals(4, cs.visibleToAbsoluteColumn(2)); // one again one.clear(1); cs = new HiddenColumns(); - cs.hideMarkedBits(one); + cs.hideColumns(one); assertEquals(1, cs.getNumberOfRegions()); - assertEquals(0, cs.adjustForHiddenColumns(0)); - assertEquals(1, cs.adjustForHiddenColumns(1)); - assertEquals(2, cs.adjustForHiddenColumns(2)); - assertEquals(4, cs.adjustForHiddenColumns(3)); + assertEquals(0, cs.visibleToAbsoluteColumn(0)); + assertEquals(1, cs.visibleToAbsoluteColumn(1)); + assertEquals(2, cs.visibleToAbsoluteColumn(2)); + assertEquals(4, cs.visibleToAbsoluteColumn(3)); } @Test(groups = { "Functional" }) @@ -746,7 +746,7 @@ public class HiddenColumnsTest assertTrue(fromMark.isEmpty()); } - hc.hideMarkedBits(toMark); + hc.hideColumns(toMark); // see if we can recover bitfield hc.markHiddenRegions(fromMark = new BitSet()); @@ -771,7 +771,7 @@ public class HiddenColumnsTest } @Test(groups = "Functional") - public void testGetVisibleStartAndEndIndexTest() + public void testGetVisibleStartAndEndIndex() { Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); AlignmentI align = new Alignment(new SequenceI[] { seq }); @@ -1009,22 +1009,22 @@ public class HiddenColumnsTest { HiddenColumns h = new HiddenColumns(); // returns input value when there are no hidden columns - assertEquals(10, h.adjustForHiddenColumns(10)); + assertEquals(10, h.visibleToAbsoluteColumn(10)); h.hideColumns(20, 30); - assertEquals(10, h.adjustForHiddenColumns(10)); - assertEquals(20 + 11, h.adjustForHiddenColumns(20)); - assertEquals(35 + 11, h.adjustForHiddenColumns(35)); + assertEquals(10, h.visibleToAbsoluteColumn(10)); + assertEquals(20 + 11, h.visibleToAbsoluteColumn(20)); + assertEquals(35 + 11, h.visibleToAbsoluteColumn(35)); h.hideColumns(5, 7); - assertEquals(10 + 3, h.adjustForHiddenColumns(10)); - assertEquals(20 + 14, h.adjustForHiddenColumns(20)); - assertEquals(35 + 14, h.adjustForHiddenColumns(35)); + assertEquals(10 + 3, h.visibleToAbsoluteColumn(10)); + assertEquals(20 + 14, h.visibleToAbsoluteColumn(20)); + assertEquals(35 + 14, h.visibleToAbsoluteColumn(35)); ColumnSelection sel = new ColumnSelection(); h.revealAllHiddenColumns(sel); h.hideColumns(0, 1); - assertEquals(4, h.adjustForHiddenColumns(2)); + assertEquals(4, h.visibleToAbsoluteColumn(2)); } @Test(groups = "Functional") @@ -1139,10 +1139,10 @@ public class HiddenColumnsTest SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT"); SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT"); - h.hideInsertionsFor(seq2); + h.hideList(seq2.getInsertions()); assertTrue(h.equals(h2)); - h.hideInsertionsFor(seq1); + h.hideList(seq1.getInsertions()); h2.hideColumns(3, 5); h2.hideColumns(9, 9); h2.hideColumns(19, 20); @@ -1156,14 +1156,14 @@ public class HiddenColumnsTest HiddenColumns h2 = new HiddenColumns(); BitSet tohide = new BitSet(21); - h.hideMarkedBits(tohide); + h.hideColumns(tohide); assertTrue(h.equals(h2)); // NB in hideMarkedBits, the last bit is not set to hidden tohide.set(3, 6); tohide.set(9); tohide.set(19, 21); - h.hideMarkedBits(tohide); + h.hideColumns(tohide); h2.hideColumns(3, 5); h2.hideColumns(9, 9);